Indonesia has added to its protests against the Abbott government's border protection policies, hauling Australia's ambassador into the foreign affairs ministry for a dressing down.

Indonesian Foreign Minister Marty Natalegawa said he had told ambassador Greg Moriarty in a meeting this week that Australia's use of lifeboats to return asylum seekers was an ''unacceptable'' escalation of its border protection policy, Indonesian news magazine Tempo reported on its website.

Fairfax Media has independently confirmed the meeting took place. The use of lifeboats has been a key development in Australia's boat turnback policy - a policy Indonesia has vehemently opposed.

The purchase of about 12 of the sophisticated lifeboats is a way of neutralising the people smugglers' tactic of deliberately scuttling boats when Australian navy or Customs ships approach, leaving the Australians no choice but to rescue the asylum seekers from the water and take them to Christmas Island.

As the opposition leading up to the September election, the Coalition defended its turnback policy, saying it would only be returning Indonesian-flagged and -crewed boats that had departed from Indonesian ports.

Dr Natalegawa said the use of lifeboats represented a more serious violation of Australia's commitments to the refugee convention than its previous policies. He said Australian ships should take the asylum seekers onboard for processing.

Customs and border protection chief Mike Pezzullo has acknowledged there is a ''public interest'' in releasing at least parts of a report into how Australian ships accidentally breached Indonesian territory.

But with Mr Pezzullo and Chief of the Defence Force David Hurley understood to be considering the report, the Customs chief refused to guarantee any of it would be released.

''I'm not going to speculate on that. There are going to be elements of this – because it relates to Operation Sovereign Borders – that are covered by the public interest immunity claim,'' Mr Pezzullo told the ABC.

But he added: ''There are going to be other matters that are in the public interest to discuss. That is to say: how did this inadvertent transgression occur? Why did it occur and what remedial action needs to be taken to ensure that it's not going to occur again?''

The government has admitted that on several occasions - Fairfax Media understands it to be about five - in December and January, Royal Australian Navy and Customs ships inadvertently crossed the 12-mile limit into Indonesian territorial waters while carrying out border protection operations.

It is understood at least some of the operations were boat turnbacks.

The Abbott government apologised to Jakarta and ordered an inquiry into how the mistakes happened. Fairfax Media understands nothing is likely to be made public at least until the end of this month.

Mr Pezzullo said he was discussing with the government and Defence what if any changes needed to be made to border protection procedures.

Prime Minister Tony Abbott on Friday reiterated an apology for breaching Indonesian territory on Fairfax radio, saying the incursions were a ''serious mistake''.

''The Indonesians have accepted our apology, but it's a serious mistake, it should have never have happened and as far as is humanly possible, we'll ensure it never happens again,'' Mr Abbott said.

Comment was being sought from Australia's Foreign Affairs department on the meeting between Dr Natalegawa and Mr Moriarty.